rs17254838

Homo sapiens
T>G
AMMECR1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0100 (2090/20864,GnomAD)
G=0054 (205/3775,1000G)
G=0182 (675/3708,TWINSUK)
G=0181 (524/2889,ALSPAC)
chrX:110228132 (GRCh38.p7) (Xq23)
AD
GWASdb2
1   publication(s)
See rs on genome
11 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr XNC_000023.11:g.110228132T>G
GRCh37.p13 chr XNC_000023.10:g.109471360T>G
AMMECR1 RefSeqGeneNG_016469.1:g.217102A>C

Gene: AMMECR1, Alport syndrome, mental retardation, midface hypoplasia and elliptocytosis chromosomal region gene 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
AMMECR1 transcript variant 2NM_001025580.1:c.N/AIntron Variant
AMMECR1 transcript variant 3NM_001171689.1:c.N/AIntron Variant
AMMECR1 transcript variant 1NM_015365.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1003T=0.998G=0.002
1000GenomesAmericanSub524T=0.930G=0.070
1000GenomesEast AsianSub764T=1.000G=0.000
1000GenomesEuropeSub766T=0.840G=0.160
1000GenomesGlobalStudy-wide3775T=0.946G=0.054
1000GenomesSouth AsianSub718T=0.940G=0.060
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide2889T=0.819G=0.181
The Genome Aggregation DatabaseAfricanSub5901T=0.979G=0.021
The Genome Aggregation DatabaseAmericanSub615T=0.930G=0.070
The Genome Aggregation DatabaseEast AsianSub1043T=1.000G=0.000
The Genome Aggregation DatabaseEuropeSub13115T=0.855G=0.144
The Genome Aggregation DatabaseGlobalStudy-wide20864T=0.899G=0.100
The Genome Aggregation DatabaseOtherSub190T=0.860G=0.140
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.818G=0.182
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs172548383.2E-05alcohol dependence20201924

eQTL of rs17254838 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs17254838 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chrX109511232109511324E06739872
chrX109511486109511536E06740126
chrX109488118109488168E06916758
chrX109488303109488489E06916943
chrX109488118109488168E07116758
chrX109488303109488489E07116943
chrX109423000109423076E072-48284
chrX109423201109423251E072-48109
chrX109423264109423365E072-47995
chrX109423401109423544E072-47816
chrX109423567109423682E072-47678